M. Khoshakhlagh, Arastoo Vojdani, A. Amali, Samaneh Abolbashari, Aida Gholoobi, Z. Meshkat
Background: A number of ribonucleic acid (RNA) and deoxyribonucleic acid (DNA) viruses commonly circulating among vertebrates, such as influenza H1N1, respiratory syncytial virus (RSV), adenoviruses, and human coronavirus (HCoV)-229E, cause symptoms similar to severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). These viruses are important causes of cold, pneumonia, and shortness of breath in humans, which have been overlooked during the coronavirus disease 2019 (COVID-19) pandemic. Furthermore, the diagnosis of infection with these viruses mostly relies on physical examination and clinical history, despite the fact that accurate molecular diagnosis is available. Objectives: This study aimed to evaluate the presence of respiratory viruses in patients who were suspected to be infected with COVID-19 yet initially tested negative for SARS-CoV-2, as it could be beneficial in developing effective control measures and more reliable testing and surveillance of such viruses. Methods: In this study, laboratory samples of 123 patients referred to Ghaem Hospital of Mashhad, Iran, were evaluated that tested negative for SARS-CoV-2 in the initial assessment while showing the clinical symptoms of COVID-19. Initial testing for SARS-CoV-2 was carried out by the TaqMan real-time polymerase chain reaction (PCR) method using a kit approved by the Ministry of Health (Pishtaz Teb, Iran). Further analysis for the presence of 17 respiratory viruses was carried out using Genova kits based on the virus genome conserved sequences of influenza H1N1, influenza B, influenza A, SARS-CoV-2, HCoV-HKU1, HCoV-OC43, HCoV-NL63, HCoV-229E, metapneumovirus, RSV, human bocavirus 1, 2, 3, parainfluenza 1, 2, 3, and adenovirus. Results: According to the results of the present evaluations, out of 123 samples that were acquired using nasal and throat swabs and that initially tested negative for SARS-CoV-2, 8 cases of influenza A (47.1%), 1 case of parainfluenza (5.9%), 1 case of HKU1/OC-43 (5.9%), 4 cases of RSV (23.5%), 1 case of HCoV-NL63/HCoV-229-E (5.9%), and 2 cases of SARS-CoV-2 (11.8%) were detected. Conclusions: Based on the results of real-time PCR tests obtained from patients who had clinical symptoms of SARS-CoV-2 infections, it can be mentioned that due to the similar symptoms of patients with respiratory viral infections, individuals with respiratory symptoms could be examined for other viral infections in addition to SARS-CoV-2 infection, and a suitable basis for their prevalence in the community could be provided.
{"title":"Evaluation of Viral Respiratory Pathogens Among Patients Initially Tested Negative for SARS-CoV-2","authors":"M. Khoshakhlagh, Arastoo Vojdani, A. Amali, Samaneh Abolbashari, Aida Gholoobi, Z. Meshkat","doi":"10.5812/jjm-136617","DOIUrl":"https://doi.org/10.5812/jjm-136617","url":null,"abstract":"Background: A number of ribonucleic acid (RNA) and deoxyribonucleic acid (DNA) viruses commonly circulating among vertebrates, such as influenza H1N1, respiratory syncytial virus (RSV), adenoviruses, and human coronavirus (HCoV)-229E, cause symptoms similar to severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). These viruses are important causes of cold, pneumonia, and shortness of breath in humans, which have been overlooked during the coronavirus disease 2019 (COVID-19) pandemic. Furthermore, the diagnosis of infection with these viruses mostly relies on physical examination and clinical history, despite the fact that accurate molecular diagnosis is available. Objectives: This study aimed to evaluate the presence of respiratory viruses in patients who were suspected to be infected with COVID-19 yet initially tested negative for SARS-CoV-2, as it could be beneficial in developing effective control measures and more reliable testing and surveillance of such viruses. Methods: In this study, laboratory samples of 123 patients referred to Ghaem Hospital of Mashhad, Iran, were evaluated that tested negative for SARS-CoV-2 in the initial assessment while showing the clinical symptoms of COVID-19. Initial testing for SARS-CoV-2 was carried out by the TaqMan real-time polymerase chain reaction (PCR) method using a kit approved by the Ministry of Health (Pishtaz Teb, Iran). Further analysis for the presence of 17 respiratory viruses was carried out using Genova kits based on the virus genome conserved sequences of influenza H1N1, influenza B, influenza A, SARS-CoV-2, HCoV-HKU1, HCoV-OC43, HCoV-NL63, HCoV-229E, metapneumovirus, RSV, human bocavirus 1, 2, 3, parainfluenza 1, 2, 3, and adenovirus. Results: According to the results of the present evaluations, out of 123 samples that were acquired using nasal and throat swabs and that initially tested negative for SARS-CoV-2, 8 cases of influenza A (47.1%), 1 case of parainfluenza (5.9%), 1 case of HKU1/OC-43 (5.9%), 4 cases of RSV (23.5%), 1 case of HCoV-NL63/HCoV-229-E (5.9%), and 2 cases of SARS-CoV-2 (11.8%) were detected. Conclusions: Based on the results of real-time PCR tests obtained from patients who had clinical symptoms of SARS-CoV-2 infections, it can be mentioned that due to the similar symptoms of patients with respiratory viral infections, individuals with respiratory symptoms could be examined for other viral infections in addition to SARS-CoV-2 infection, and a suitable basis for their prevalence in the community could be provided.","PeriodicalId":17803,"journal":{"name":"Jundishapur Journal of Microbiology","volume":" ","pages":""},"PeriodicalIF":0.6,"publicationDate":"2023-08-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"48492590","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
W. Shen, Jingjing Sheng, Meng Wang, Xiujiao Xia, Keyu Ling, M. Qian, Zhejiong Wang, P. Du
Background: Candida is the main causative agent of severe mucosal and invasive candidiasis. Different species of Candida have shown varying levels of resistance to antifungal treatments. It is estimated that each 12-hour delay in antifungal treatment is associated with a significant increase in patient mortality and treatment costs. The culture method is regarded as the gold standard for identifying Candida species, but its time-consuming process is a clear disadvantage. Objectives: This study established a method using membrane technology combined with dual-target melting analysis for rapid cultivation and identification of common Candida species. This method is expected to preserve the advantages of the conventional culture method and improve upon its weaknesses while also evaluating the practical application of the method. Methods: A microfiltration membrane-based culture followed by a color indicator method was established to rapidly cultivate Candida cultures. The 5.8S ribosomal DNA region and internal transcribed spacer 2 (ITS2) region were used as target gene regions, for which two sets of primers were employed. Melting analysis following dual-target real-time polymerase chain reaction (PCR) was conducted to distinguish among Candida albicans, C. tropicalis, C. glabrata, and C. krusei. To evaluate its practical application, the method was tested with 72 clinical isolates, and the results were compared with those obtained using the chromogenic culture method and DNA sequencing. Results: Distinctive melting temperatures in the two gene targets were detected among the four common Candida species. The entire process, from cultivation to identification, was completed within 12 hours, about 50% less time than the gold-standard method. The minimum detection limit of Candida species was 10 femtograms. The results of the identification of the clinical isolates were consistent with those of DNA sequencing. Conclusions: The short-term membrane-based cultivation combined with dual-target melting analysis can be used to rapidly, easily, and accurately identify common Candida species, thus reducing the time needed to initiate targeted treatment for patients with severe candidiasis.
{"title":"Development of Short-term Membrane-based Cultivation Combined with Dual-target Melting Analysis for Rapid Differentiation of Common Candida Species","authors":"W. Shen, Jingjing Sheng, Meng Wang, Xiujiao Xia, Keyu Ling, M. Qian, Zhejiong Wang, P. Du","doi":"10.5812/jjm-136710","DOIUrl":"https://doi.org/10.5812/jjm-136710","url":null,"abstract":"Background: Candida is the main causative agent of severe mucosal and invasive candidiasis. Different species of Candida have shown varying levels of resistance to antifungal treatments. It is estimated that each 12-hour delay in antifungal treatment is associated with a significant increase in patient mortality and treatment costs. The culture method is regarded as the gold standard for identifying Candida species, but its time-consuming process is a clear disadvantage. Objectives: This study established a method using membrane technology combined with dual-target melting analysis for rapid cultivation and identification of common Candida species. This method is expected to preserve the advantages of the conventional culture method and improve upon its weaknesses while also evaluating the practical application of the method. Methods: A microfiltration membrane-based culture followed by a color indicator method was established to rapidly cultivate Candida cultures. The 5.8S ribosomal DNA region and internal transcribed spacer 2 (ITS2) region were used as target gene regions, for which two sets of primers were employed. Melting analysis following dual-target real-time polymerase chain reaction (PCR) was conducted to distinguish among Candida albicans, C. tropicalis, C. glabrata, and C. krusei. To evaluate its practical application, the method was tested with 72 clinical isolates, and the results were compared with those obtained using the chromogenic culture method and DNA sequencing. Results: Distinctive melting temperatures in the two gene targets were detected among the four common Candida species. The entire process, from cultivation to identification, was completed within 12 hours, about 50% less time than the gold-standard method. The minimum detection limit of Candida species was 10 femtograms. The results of the identification of the clinical isolates were consistent with those of DNA sequencing. Conclusions: The short-term membrane-based cultivation combined with dual-target melting analysis can be used to rapidly, easily, and accurately identify common Candida species, thus reducing the time needed to initiate targeted treatment for patients with severe candidiasis.","PeriodicalId":17803,"journal":{"name":"Jundishapur Journal of Microbiology","volume":" ","pages":""},"PeriodicalIF":0.6,"publicationDate":"2023-08-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"43864803","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Parastu Satei, S. Fahimirad, E. Ghaznavi-Rad, H. Abtahi
Background: Most Acinetobacter baumannii (A. baumannii) species have become resistant to all common antibiotics. Many antimicrobial peptides (AMPs) have been identified with efficient functions in infection management. E50-52 (UniProtKB: P85148) and Ib-AMP4 (UniProtKB: O24006) AMPs have shown marked antibacterial functions. Objectives: This investigation was designed to produce E50-52 and Ib-AMP4 AMPs through recombinant protein production. Subsequently, the synergistic antimicrobial functions of these two peptides were assessed under in vitro and in vivo circumstances on multidrug-resistant A. baumannii to investigate the antimicrobial effects of Ib-AMP4 and E50-52 AMPs on drug-resistant Acinetobacter. Methods: The gene sequence of E50-52 and Ib-AMP4 AMPs were codon optimized and separately inserted into the pET-32α vector. The recombinant structures were expressed in host bacteria. The antibacterial functions of the individual and combined application of the purified refolded E50-52 and Ib-AMP4 AMPs against multidrug-resistant A. baumannii were evaluated through the time-kill, minimum inhibitory concentration (MIC), growth kinetic assays, and in vivo (mouse body) systemic infection. Results: The minimum concentrations of the produced refolded E50-52 and Ib-AMP4 AMPs against A. baumannii were 0.325 and 0.0625 mg/mL, respectively. Moreover, the checkerboard procedure confirmed the synergic effects of the produced AMPs. The use of E50-52 and Ib-AMP4 AMPs in combination resulted in an over five times reduction in log10 CFU/mL of alive cells during the first 240-min exposure. The antibacterial efficiency of the produced AMPs was confirmed by growth kinetic assays, scanning electron microscopy (SEM) results, and in vivo evaluation tests. The in vivo assay on rats confirmed the significant antibacterial functions of the produced recombinant proteins on A. baumannii systemic infection. Conclusions: The results proved the considerable synergistic antibacterial functions of the produced recombinant Ib-AMP4 and E50-52 AMPs to treat A. baumannii systemic infection effectively.
{"title":"In Vitro and In Vivo Synergistic Antibacterial Functions of the Recombinant Ib-AMP4 and E50-52 Antimicrobial Peptides against Multidrug-Resistant Acinetobacter baumannii","authors":"Parastu Satei, S. Fahimirad, E. Ghaznavi-Rad, H. Abtahi","doi":"10.5812/jjm-136280","DOIUrl":"https://doi.org/10.5812/jjm-136280","url":null,"abstract":"Background: Most Acinetobacter baumannii (A. baumannii) species have become resistant to all common antibiotics. Many antimicrobial peptides (AMPs) have been identified with efficient functions in infection management. E50-52 (UniProtKB: P85148) and Ib-AMP4 (UniProtKB: O24006) AMPs have shown marked antibacterial functions. Objectives: This investigation was designed to produce E50-52 and Ib-AMP4 AMPs through recombinant protein production. Subsequently, the synergistic antimicrobial functions of these two peptides were assessed under in vitro and in vivo circumstances on multidrug-resistant A. baumannii to investigate the antimicrobial effects of Ib-AMP4 and E50-52 AMPs on drug-resistant Acinetobacter. Methods: The gene sequence of E50-52 and Ib-AMP4 AMPs were codon optimized and separately inserted into the pET-32α vector. The recombinant structures were expressed in host bacteria. The antibacterial functions of the individual and combined application of the purified refolded E50-52 and Ib-AMP4 AMPs against multidrug-resistant A. baumannii were evaluated through the time-kill, minimum inhibitory concentration (MIC), growth kinetic assays, and in vivo (mouse body) systemic infection. Results: The minimum concentrations of the produced refolded E50-52 and Ib-AMP4 AMPs against A. baumannii were 0.325 and 0.0625 mg/mL, respectively. Moreover, the checkerboard procedure confirmed the synergic effects of the produced AMPs. The use of E50-52 and Ib-AMP4 AMPs in combination resulted in an over five times reduction in log10 CFU/mL of alive cells during the first 240-min exposure. The antibacterial efficiency of the produced AMPs was confirmed by growth kinetic assays, scanning electron microscopy (SEM) results, and in vivo evaluation tests. The in vivo assay on rats confirmed the significant antibacterial functions of the produced recombinant proteins on A. baumannii systemic infection. Conclusions: The results proved the considerable synergistic antibacterial functions of the produced recombinant Ib-AMP4 and E50-52 AMPs to treat A. baumannii systemic infection effectively.","PeriodicalId":17803,"journal":{"name":"Jundishapur Journal of Microbiology","volume":" ","pages":""},"PeriodicalIF":0.6,"publicationDate":"2023-08-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"44651283","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Background: Colorectal cancer (CRC) is the third most common cancer worldwide, and its development is influenced by genetic and environmental factors, including the gut microbiota. Recent studies have reported an association between Fusobacterium nucleatum abundance and CRC. Objectives: This study aimed to investigate the abundance of F. nucleatum in CRC and polyp patients and its association with the expression of Chemokine ligand -3(CCL3), Vascular endothelial growth factor (VEGF), and Nuclear factor-kappa B (NF-KB11) genes and the presence of deoxyribonucleic acid (DNA) mutations and polymorphisms in the Kirsten rat sarcoma viral oncogene homolog (KRAS) gene. Methods: A total of 80 biopsy samples were collected from CRC, polyp, and colitis patients. Moreover, F. nucleatum abundance was measured by quantitative polymerase chain reaction (qPCR). The expression of CCL3, VEGF, and NF-KB11 genes was measured by reverse transcription polymerase chain reaction (RT-PCR). Additionally, KRAS gene mutations and polymorphisms were detected by the Mutation Surveyor software (V5.1.2). Results: The results showed that F. nucleatum abundance was significantly higher in CRC and polyp patients than in colitis patients (P < 0.05). The expression of CCL3 and VEGF genes was also significantly higher in F. nucleatum-positive samples (P < 0.05). However, NF-KB11 gene expression was non-significant. F. nucleatum-positive biopsy samples had a higher frequency of KRAS gene mutations and polymorphisms than F. nucleatum-negative CRC patients (odds ratio = 3). Most of the mutations observed in the positive samples were (6144A>AT,31E>E) at exon 2 of the KRAS gene. Conclusions: The study findings suggest that F. nucleatum might play a role in CRC and polyp development and contribute to KRAS gene mutations. Therefore, targeting F. nucleatum in the gut microbiota could be a potential therapeutic strategy for preventing CRC and polyp development.
{"title":"Fusobacterium nucleatum-Mediated Alteration in Expression of VEGF and CCL3 Genes and KRAS Mutation in Colorectal Cancer Patients","authors":"H. J. Taher, F. Kamel","doi":"10.5812/jjm-136914","DOIUrl":"https://doi.org/10.5812/jjm-136914","url":null,"abstract":"Background: Colorectal cancer (CRC) is the third most common cancer worldwide, and its development is influenced by genetic and environmental factors, including the gut microbiota. Recent studies have reported an association between Fusobacterium nucleatum abundance and CRC. Objectives: This study aimed to investigate the abundance of F. nucleatum in CRC and polyp patients and its association with the expression of Chemokine ligand -3(CCL3), Vascular endothelial growth factor (VEGF), and Nuclear factor-kappa B (NF-KB11) genes and the presence of deoxyribonucleic acid (DNA) mutations and polymorphisms in the Kirsten rat sarcoma viral oncogene homolog (KRAS) gene. Methods: A total of 80 biopsy samples were collected from CRC, polyp, and colitis patients. Moreover, F. nucleatum abundance was measured by quantitative polymerase chain reaction (qPCR). The expression of CCL3, VEGF, and NF-KB11 genes was measured by reverse transcription polymerase chain reaction (RT-PCR). Additionally, KRAS gene mutations and polymorphisms were detected by the Mutation Surveyor software (V5.1.2). Results: The results showed that F. nucleatum abundance was significantly higher in CRC and polyp patients than in colitis patients (P < 0.05). The expression of CCL3 and VEGF genes was also significantly higher in F. nucleatum-positive samples (P < 0.05). However, NF-KB11 gene expression was non-significant. F. nucleatum-positive biopsy samples had a higher frequency of KRAS gene mutations and polymorphisms than F. nucleatum-negative CRC patients (odds ratio = 3). Most of the mutations observed in the positive samples were (6144A>AT,31E>E) at exon 2 of the KRAS gene. Conclusions: The study findings suggest that F. nucleatum might play a role in CRC and polyp development and contribute to KRAS gene mutations. Therefore, targeting F. nucleatum in the gut microbiota could be a potential therapeutic strategy for preventing CRC and polyp development.","PeriodicalId":17803,"journal":{"name":"Jundishapur Journal of Microbiology","volume":" ","pages":""},"PeriodicalIF":0.6,"publicationDate":"2023-07-31","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"46561793","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Background: SARS-CoV-2 is a single-stranded RNA virus and a member of a large family of Coronaviruses that are important human pathogens. This virus caused severe acute respiratory syndrome and was initially identified to be transmitted between humans on November 17, 2019. Objectives: To investigate the lineage, mutational patterns, variants, and serotypes of SARS-CoV-2 viruses circulating in the Duhok governorate population and to compare them with those identified in travelers crossing the border from Turkey in order to trace the epidemiological patterns. Methods: Nasopharyngeal swabs were collected from 700 individuals living in Duhok and 700 travelers crossing the border to Duhok-Iraq from Turkey. The subjects were recruited by random sampling and questioned about demographic features and symptoms of upper or lower respiratory tract infections. Exclusion criteria included vaccination with COVID-19 vaccines of any approved previous infection. Samples were subjected to RT-PCR (QIAGEN KIT), and 30 positive samples with the highest viral load (lowest Ct values) were chosen for sequencing of the complete S gene by next-generation sequencing (NGS) (INTERGEN Genetics and Rare Diseases Diagnosis Research and Application Center, Turkey). Three platforms of Nextstrain, GISAID, and PANGO were used to identify variants, clades, and lineages and analyze sequences. Results: Out of 1400 participants, 353 (25.21%) positive samples were identified by RT-PCR, of which 30 representative positive samples (15 from each group: Patients and travelers) were sent for complete sequencing of the S spike gene using NGS. Nineteen samples were successfully sequenced and retrieved, including nine samples from Duhok residents and ten samples from travelers. Nextclade results revealed that 12 samples belonged to the delta strain (Pango lineages: B1.617.2.78, B1.617.2, B1.617.126, and B.1.617.121) distributed among the two groups while 5 omicron (BA.1.1) and 2 alpha (B.1.1.7) strains were found among travelers. A total of 76 mutations, including 52 non-synonymous, 16 synonymous, and 8 deletions, were detected without identifying a unique mutation. Sequencing results were submitted to GISAID, and accession numbers were obtained. A phylogenetic tree was constructed using the sequences obtained from Iraqi and non-Iraqi variants from GISAID. Conclusions: The present research presents a description and observation of the genetic and epigenetic status of SARS-CoV-2 in Iraq based on sequencing results. The study revealed the impact of travels in introducing new variants to the country, including those with mutations in the S1 domain of the spike protein that can enhance viral attachment to receptors.
{"title":"Comparison of Sequencing and Phylogenetic Analysis of SARS-CoV-2 Spike Proteins Extracted from Patients and Travelers in Duhok-Iraq","authors":"Omar Mohammed Younus, A. Parmaksız, A. Goreal","doi":"10.5812/jjm-138053","DOIUrl":"https://doi.org/10.5812/jjm-138053","url":null,"abstract":"Background: SARS-CoV-2 is a single-stranded RNA virus and a member of a large family of Coronaviruses that are important human pathogens. This virus caused severe acute respiratory syndrome and was initially identified to be transmitted between humans on November 17, 2019. Objectives: To investigate the lineage, mutational patterns, variants, and serotypes of SARS-CoV-2 viruses circulating in the Duhok governorate population and to compare them with those identified in travelers crossing the border from Turkey in order to trace the epidemiological patterns. Methods: Nasopharyngeal swabs were collected from 700 individuals living in Duhok and 700 travelers crossing the border to Duhok-Iraq from Turkey. The subjects were recruited by random sampling and questioned about demographic features and symptoms of upper or lower respiratory tract infections. Exclusion criteria included vaccination with COVID-19 vaccines of any approved previous infection. Samples were subjected to RT-PCR (QIAGEN KIT), and 30 positive samples with the highest viral load (lowest Ct values) were chosen for sequencing of the complete S gene by next-generation sequencing (NGS) (INTERGEN Genetics and Rare Diseases Diagnosis Research and Application Center, Turkey). Three platforms of Nextstrain, GISAID, and PANGO were used to identify variants, clades, and lineages and analyze sequences. Results: Out of 1400 participants, 353 (25.21%) positive samples were identified by RT-PCR, of which 30 representative positive samples (15 from each group: Patients and travelers) were sent for complete sequencing of the S spike gene using NGS. Nineteen samples were successfully sequenced and retrieved, including nine samples from Duhok residents and ten samples from travelers. Nextclade results revealed that 12 samples belonged to the delta strain (Pango lineages: B1.617.2.78, B1.617.2, B1.617.126, and B.1.617.121) distributed among the two groups while 5 omicron (BA.1.1) and 2 alpha (B.1.1.7) strains were found among travelers. A total of 76 mutations, including 52 non-synonymous, 16 synonymous, and 8 deletions, were detected without identifying a unique mutation. Sequencing results were submitted to GISAID, and accession numbers were obtained. A phylogenetic tree was constructed using the sequences obtained from Iraqi and non-Iraqi variants from GISAID. Conclusions: The present research presents a description and observation of the genetic and epigenetic status of SARS-CoV-2 in Iraq based on sequencing results. The study revealed the impact of travels in introducing new variants to the country, including those with mutations in the S1 domain of the spike protein that can enhance viral attachment to receptors.","PeriodicalId":17803,"journal":{"name":"Jundishapur Journal of Microbiology","volume":" ","pages":""},"PeriodicalIF":0.6,"publicationDate":"2023-07-29","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"41794628","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Farzad Mohammadi Ebli, Z. Heshmatipour, K. Daneshjou, S. Siadat
Background: Nosocomial infections have increased among patients admitted to the intensive care unit (ICU). Objectives: This study investigated the microbiota pattern of the respiratory system in hospitalized patients with treatment-resistant respiratory infections compared to those without treatment-resistant respiratory infections. Methods: This case-control study utilized sputum samples from hospital-acquired infection (HAI) and non-HAI (NHAI) patients over 52 years old hospitalized in the ICU. Identification and determination of the drug sensitivity of the bacteria responsible for treatment-resistant respiratory infections were made by culture method in selective and differential media and VITEK 2 device. Finally, quantitative polymerase chain reaction (qPCR) was used to analyze the microbiota of the respiratory system. Results: Excessive prescription of antibiotics, long hospitalization, and history of surgery were important risk factors for nosocomial infections. The study of antibiotic resistance of pathogens causing hospital infections indicated their high resistance to most common antibiotics. Also, nosocomial infections led to a change in lung microbiota in HAI patients. The frequencies of Streptococcus pyogenes, S. pneumoniae, and Haemophilus influenzae were higher in patients with treatment-resistant respiratory infection (P < 0.05), but the frequency of Neisseria spp. was higher in patients without treatment-resistant respiratory infection (P < 0.05). Conclusions: The pathogens responsible for nosocomial infections had acquired resistance to a wide range of antibiotics, leading to changes in their respiratory microbiota.
{"title":"Comparison of Respiratory Microbiota in Patients with and Without Hospital-Acquired Infection","authors":"Farzad Mohammadi Ebli, Z. Heshmatipour, K. Daneshjou, S. Siadat","doi":"10.5812/jjm-133257","DOIUrl":"https://doi.org/10.5812/jjm-133257","url":null,"abstract":"Background: Nosocomial infections have increased among patients admitted to the intensive care unit (ICU). Objectives: This study investigated the microbiota pattern of the respiratory system in hospitalized patients with treatment-resistant respiratory infections compared to those without treatment-resistant respiratory infections. Methods: This case-control study utilized sputum samples from hospital-acquired infection (HAI) and non-HAI (NHAI) patients over 52 years old hospitalized in the ICU. Identification and determination of the drug sensitivity of the bacteria responsible for treatment-resistant respiratory infections were made by culture method in selective and differential media and VITEK 2 device. Finally, quantitative polymerase chain reaction (qPCR) was used to analyze the microbiota of the respiratory system. Results: Excessive prescription of antibiotics, long hospitalization, and history of surgery were important risk factors for nosocomial infections. The study of antibiotic resistance of pathogens causing hospital infections indicated their high resistance to most common antibiotics. Also, nosocomial infections led to a change in lung microbiota in HAI patients. The frequencies of Streptococcus pyogenes, S. pneumoniae, and Haemophilus influenzae were higher in patients with treatment-resistant respiratory infection (P < 0.05), but the frequency of Neisseria spp. was higher in patients without treatment-resistant respiratory infection (P < 0.05). Conclusions: The pathogens responsible for nosocomial infections had acquired resistance to a wide range of antibiotics, leading to changes in their respiratory microbiota.","PeriodicalId":17803,"journal":{"name":"Jundishapur Journal of Microbiology","volume":" ","pages":""},"PeriodicalIF":0.6,"publicationDate":"2023-07-29","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"45297229","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
M. Nakhaie, E. Taheri, J. Charostad, Nasir Arefinia, D. Kalantar-Neyestanaki, Mohammad Rezaei Zadeh Rukerd, F. Ahmadpour, Mohamad Hossein Pourebrahimi, Sara Ahmadinejad Farsangi, Sara Shafieipour
Background: Hepatitis C virus (HCV) is one of the most common infections in hemodialysis patients, which has been associated with increased incidence of morbidity and mortality, particularly in low- and middle-income countries. Objectives: The current study aimed to evaluate the HCV antibody, occult HCV infection (OCI), and related risk factors among hemodialysis patients. Methods: In this cross-sectional study, 100 hemodialysis patients referred to a dialysis center in Kerman between December 2021 and March 2022 were assessed for HCV, OCI, and their related risk factors. The information related to risk factors was collected by questionnaire, while HCV and OCI were detected through serology and real-time polymerase chain reaction (PCR) methods, respectively. Results: Among the patients participating in the study, 61 were men, and 39 were women. The average age was 58.1 ± 14.9 years in men and 63.6 ± 11.4 years in women. Diabetes and hypertension history, old age, low education, self-employment, and urban living were more common in chronic kidney disease patients. The enzyme-linked immunosorbent assay (ELISA) revealed 3% positive seroprevalence HCV infection, but only 1% was positive for OCI. Although no statistically significant relationship was found between the presence of HCV (antibody and OCI) and other parameters, all positive HCV cases were identified in patients with low education and freelance employment. Conclusions: Hemodialysis patients had a low prevalence of HCV antibody and OCI. Improving various factors and conditions such as lifestyle, occupation, educational level, and dialysis ward and machine disinfection could be beneficial in managing and controlling hemodialysis complications such as HCV and OCI.
{"title":"Prevalence of Hepatitis C Virus and Its Occult Infection in Hemodialysis Patients","authors":"M. Nakhaie, E. Taheri, J. Charostad, Nasir Arefinia, D. Kalantar-Neyestanaki, Mohammad Rezaei Zadeh Rukerd, F. Ahmadpour, Mohamad Hossein Pourebrahimi, Sara Ahmadinejad Farsangi, Sara Shafieipour","doi":"10.5812/jjm-136504","DOIUrl":"https://doi.org/10.5812/jjm-136504","url":null,"abstract":"Background: Hepatitis C virus (HCV) is one of the most common infections in hemodialysis patients, which has been associated with increased incidence of morbidity and mortality, particularly in low- and middle-income countries. Objectives: The current study aimed to evaluate the HCV antibody, occult HCV infection (OCI), and related risk factors among hemodialysis patients. Methods: In this cross-sectional study, 100 hemodialysis patients referred to a dialysis center in Kerman between December 2021 and March 2022 were assessed for HCV, OCI, and their related risk factors. The information related to risk factors was collected by questionnaire, while HCV and OCI were detected through serology and real-time polymerase chain reaction (PCR) methods, respectively. Results: Among the patients participating in the study, 61 were men, and 39 were women. The average age was 58.1 ± 14.9 years in men and 63.6 ± 11.4 years in women. Diabetes and hypertension history, old age, low education, self-employment, and urban living were more common in chronic kidney disease patients. The enzyme-linked immunosorbent assay (ELISA) revealed 3% positive seroprevalence HCV infection, but only 1% was positive for OCI. Although no statistically significant relationship was found between the presence of HCV (antibody and OCI) and other parameters, all positive HCV cases were identified in patients with low education and freelance employment. Conclusions: Hemodialysis patients had a low prevalence of HCV antibody and OCI. Improving various factors and conditions such as lifestyle, occupation, educational level, and dialysis ward and machine disinfection could be beneficial in managing and controlling hemodialysis complications such as HCV and OCI.","PeriodicalId":17803,"journal":{"name":"Jundishapur Journal of Microbiology","volume":" ","pages":""},"PeriodicalIF":0.6,"publicationDate":"2023-07-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"47790979","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Samaneh Salarvand, A. Abdollahi, Masoumeh Doraghi, Seyed Amir Miratashi Yazdi, Z. Panahi, S. Mortazavi, E. Nazar
Background: Patients undergoing orthopedic surgery are at risk of nosocomial infections, and antibiotic resistance is known to increase the risk of such infections. Objectives: We aimed to determine the rate of antibiotic resistance in patients admitted to orthopedic wards in one of the largest referral hospitals in Iran. We also ascertained responsible antibiotic-resistant microorganisms in patients with bone and joint infections. Methods: The present cross-sectional investigation was concluded over a period of five years, from March 2018 to March 2022, at a great referral hospital in Tehran. Laboratory data, including the organisms isolated and their antibiotic resistance patterns, were collected by reviewing the hospital information system. Results: In total, 2650 specimens obtained from patients with suspected bacterial infections were transferred to the hospital’s laboratory, 880 (33.2%) of which were positive for bacterial infections. The maximum antibiotic resistance rate against an antibiotic was observed to be 58% for Staphylococcus aureus (erythromycin), 75% for Klebsiella pneumonia (ampicillin/sulbactam), 64.5% for Escherichia coli (imipenem), 76.2% for coagulase-negative Staphylococcus (vancomycin), 100% for Acinetobacter baumannii (imipenem), 52% for S. epidermidis (erythromycin), 85.9% for Enterobacter species (gentamycin), and 65.6% for Pseudomonas aeruginosa (ampicillin/sulbactam). The overall rate of multi-drug resistance was obtained as 27.6%. Conclusions: A high rate of resistance of various bacterial strains to common antibiotics, especially erythromycin, ampicillin, imipenem, vancomycin, and gentamycin, was denoted in orthopedic wards. Also, a high rate of multi-antibiotic resistance was encountered in these wards, where more than a quarter of the bacterial strains showed such resistance.
{"title":"Microbiological Profile and Drug Resistance in Bone and Joint Infections: A Survey in Orthopedic Wards of a Great Referral Hospital in Tehran, Iran","authors":"Samaneh Salarvand, A. Abdollahi, Masoumeh Doraghi, Seyed Amir Miratashi Yazdi, Z. Panahi, S. Mortazavi, E. Nazar","doi":"10.5812/jjm-137125","DOIUrl":"https://doi.org/10.5812/jjm-137125","url":null,"abstract":"Background: Patients undergoing orthopedic surgery are at risk of nosocomial infections, and antibiotic resistance is known to increase the risk of such infections. Objectives: We aimed to determine the rate of antibiotic resistance in patients admitted to orthopedic wards in one of the largest referral hospitals in Iran. We also ascertained responsible antibiotic-resistant microorganisms in patients with bone and joint infections. Methods: The present cross-sectional investigation was concluded over a period of five years, from March 2018 to March 2022, at a great referral hospital in Tehran. Laboratory data, including the organisms isolated and their antibiotic resistance patterns, were collected by reviewing the hospital information system. Results: In total, 2650 specimens obtained from patients with suspected bacterial infections were transferred to the hospital’s laboratory, 880 (33.2%) of which were positive for bacterial infections. The maximum antibiotic resistance rate against an antibiotic was observed to be 58% for Staphylococcus aureus (erythromycin), 75% for Klebsiella pneumonia (ampicillin/sulbactam), 64.5% for Escherichia coli (imipenem), 76.2% for coagulase-negative Staphylococcus (vancomycin), 100% for Acinetobacter baumannii (imipenem), 52% for S. epidermidis (erythromycin), 85.9% for Enterobacter species (gentamycin), and 65.6% for Pseudomonas aeruginosa (ampicillin/sulbactam). The overall rate of multi-drug resistance was obtained as 27.6%. Conclusions: A high rate of resistance of various bacterial strains to common antibiotics, especially erythromycin, ampicillin, imipenem, vancomycin, and gentamycin, was denoted in orthopedic wards. Also, a high rate of multi-antibiotic resistance was encountered in these wards, where more than a quarter of the bacterial strains showed such resistance.","PeriodicalId":17803,"journal":{"name":"Jundishapur Journal of Microbiology","volume":" ","pages":""},"PeriodicalIF":0.6,"publicationDate":"2023-07-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"45885285","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Background: The composition of lung tissue microorganisms in patients with different tissue types of lung cancer has not yet been determined. Previous studies have shown changes in the composition of pulmonary microbial flora in patients with lung cancer. Objectives: This study aimed to investigate the differences and correlations in the microbial flora of pulmonary tissue among different histological types of lung cancer. Methods: Samples of tumor and normal lung tissue from 29 patients with early-stage lung cancer were collected. The samples were sequenced using Illumina HiSeq high throughput sequencing technology for 16S rDNA in the V4 region of the bacteria. Also, their microbiological characteristics were detected, and bioinformatics analysis was performed. Results: The results of microbial abundance analysis in the lung tissue of patients with lung cancer showed that the bacterial colony composition of the two tissues was similar, with Proteobacteria, Thickwalled Bacteria, Anomalococcus, Bacteroides, and Actinobacteria predominating. Analysis of microbial diversity found no difference in α diversity and β diversity between normal lung tissue and tumor tissue. When analyzing patients with adenocarcinoma, the abundance of Micrococcales and Blastomonas was significantly higher in tumor tissue than in normal lung tissue. Conclusions: The composition of microbial flora in different parts of lung tissue of early-stage lung cancer patients is consistent, but the dominant flora varies among different histological types of lung cancer.
{"title":"Microbial Diversity and Abundance in Pulmonary Tissue of Patients with Early-Stage Lung Cancer","authors":"Zhao Shouhua, L. Meilan","doi":"10.5812/jjm-137478","DOIUrl":"https://doi.org/10.5812/jjm-137478","url":null,"abstract":"Background: The composition of lung tissue microorganisms in patients with different tissue types of lung cancer has not yet been determined. Previous studies have shown changes in the composition of pulmonary microbial flora in patients with lung cancer. Objectives: This study aimed to investigate the differences and correlations in the microbial flora of pulmonary tissue among different histological types of lung cancer. Methods: Samples of tumor and normal lung tissue from 29 patients with early-stage lung cancer were collected. The samples were sequenced using Illumina HiSeq high throughput sequencing technology for 16S rDNA in the V4 region of the bacteria. Also, their microbiological characteristics were detected, and bioinformatics analysis was performed. Results: The results of microbial abundance analysis in the lung tissue of patients with lung cancer showed that the bacterial colony composition of the two tissues was similar, with Proteobacteria, Thickwalled Bacteria, Anomalococcus, Bacteroides, and Actinobacteria predominating. Analysis of microbial diversity found no difference in α diversity and β diversity between normal lung tissue and tumor tissue. When analyzing patients with adenocarcinoma, the abundance of Micrococcales and Blastomonas was significantly higher in tumor tissue than in normal lung tissue. Conclusions: The composition of microbial flora in different parts of lung tissue of early-stage lung cancer patients is consistent, but the dominant flora varies among different histological types of lung cancer.","PeriodicalId":17803,"journal":{"name":"Jundishapur Journal of Microbiology","volume":" ","pages":""},"PeriodicalIF":0.6,"publicationDate":"2023-07-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"41420017","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Background: NAP1/027 Clostridium difficile infection (CDI) has rarely been reported in China. Objectives: The objective of this study was to strengthen the understanding of the risk factors and outcomes of NAP1/027 CDI. Methods: A single-center, retrospective, case-control (1: 3) study was performed to identify risk factors and outcomes specific to NAP1/027 CDI using a group of patients with NAP1/027 CDI (n = 20) and a group of age-matched control patients with non-NAP1/027 CDI (n = 60) within June 2018 and August 2021. The patient charts were thoroughly reviewed to assess the markers of severity, risk factors, and outcomes. Results: Out of the 272 stool specimens, 41 cases (15.07%) tested positive for the NAP1 strain of C. difficile using the polymerase chain reaction. Among these specimens, 20 cases fulfilled the inclusion criteria. No significant difference was observed between the NAP1/027 and non-NAP1/027 groups in disease severity, length of hospital stay, or mortality. Logistic regression analysis revealed that risk factors for acquiring NAP1/027 infection included hospitalization in the 90 days before CDI diagnosis and high C-reactive protein level within ± 3 days of C. difficile detection. Conclusions: In a large non-epidemic tertiary hospital in China, NAP1/027 strains were more prevalent in patients with previous hospitalization and high CRP level than non-NAP1/027 strains.
{"title":"Clostridium difficile Infection Risk Factors and Outcomes Among Inpatients Infected with NAP1/BI/027 Strain Compared to Non-NAP1 Strain in a Major Chinese Hospital","authors":"Guangyue Yao, Wenjia Wang, Chunhong Shao, Jing Shao, Hui Fan, Yuanyuan Bai","doi":"10.5812/jjm-136904","DOIUrl":"https://doi.org/10.5812/jjm-136904","url":null,"abstract":"Background: NAP1/027 Clostridium difficile infection (CDI) has rarely been reported in China. Objectives: The objective of this study was to strengthen the understanding of the risk factors and outcomes of NAP1/027 CDI. Methods: A single-center, retrospective, case-control (1: 3) study was performed to identify risk factors and outcomes specific to NAP1/027 CDI using a group of patients with NAP1/027 CDI (n = 20) and a group of age-matched control patients with non-NAP1/027 CDI (n = 60) within June 2018 and August 2021. The patient charts were thoroughly reviewed to assess the markers of severity, risk factors, and outcomes. Results: Out of the 272 stool specimens, 41 cases (15.07%) tested positive for the NAP1 strain of C. difficile using the polymerase chain reaction. Among these specimens, 20 cases fulfilled the inclusion criteria. No significant difference was observed between the NAP1/027 and non-NAP1/027 groups in disease severity, length of hospital stay, or mortality. Logistic regression analysis revealed that risk factors for acquiring NAP1/027 infection included hospitalization in the 90 days before CDI diagnosis and high C-reactive protein level within ± 3 days of C. difficile detection. Conclusions: In a large non-epidemic tertiary hospital in China, NAP1/027 strains were more prevalent in patients with previous hospitalization and high CRP level than non-NAP1/027 strains.","PeriodicalId":17803,"journal":{"name":"Jundishapur Journal of Microbiology","volume":" ","pages":""},"PeriodicalIF":0.6,"publicationDate":"2023-07-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"42625789","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
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